Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 311,523 C→T 28.7% S450S (TCG→TCA)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,5230CT28.7% 179.8 / 71.1 105S450S (TCG→TCA) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (36/38);  new base T (14/16);  total (51/54)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

Only 100 of 107 total aligned reads displayed.

GTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCT  >  minE/311455‑311589
                                                                    |                                                                  
gTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa                                                                  <  1:2636719/71‑1 (MQ=255)
   aTAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                                               >  1:4973468/1‑71 (MQ=255)
   aTAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                                               >  1:5367023/1‑71 (MQ=255)
    tAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACa                                                                <  1:679377/69‑1 (MQ=255)
     agagAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa                                                                  <  1:788602/66‑1 (MQ=255)
     agagAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTa                                                             >  1:1350901/1‑71 (MQ=255)
        gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                          <  1:4286376/71‑1 (MQ=255)
        gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                          <  1:3284158/71‑1 (MQ=255)
        gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                          <  1:1460261/71‑1 (MQ=255)
         aaCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt                                                         <  1:3447088/71‑1 (MQ=9)
          aCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt                                                         <  1:2281518/70‑1 (MQ=9)
          aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATc                                                        <  1:567990/71‑1 (MQ=255)
           cTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcg                                                       >  1:3512703/1‑71 (MQ=255)
              gcGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                                    <  1:2261693/70‑1 (MQ=12)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                            <  1:4104221/63‑1 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                            <  1:2462337/63‑1 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                            <  1:4097488/63‑1 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                            <  1:13856/63‑1 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                                     <  1:372901/70‑1 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                                     <  1:61448/70‑1 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgc                                                      <  1:4589323/69‑1 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                                    >  1:2999704/1‑71 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                                    >  1:3048474/1‑71 (MQ=255)
              aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                                    >  1:3423818/1‑71 (MQ=255)
                gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGAt                                                   <  1:5466771/70‑1 (MQ=255)
                gataaattGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATa                                                  <  1:4363444/71‑1 (MQ=255)
                    gatagCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGa                                              >  1:2544643/1‑71 (MQ=255)
                       agCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGAc                                             >  1:2910826/1‑69 (MQ=255)
                        gccccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATa                                                  >  1:3179630/4‑63 (MQ=12)
                        gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                           <  1:1459092/70‑1 (MQ=255)
                        gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                           <  1:4451474/70‑1 (MQ=255)
                          cccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCAcc                                                           <  1:1448029/51‑1 (MQ=12)
                          cccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCAcc                                                           <  1:5367771/51‑1 (MQ=12)
                            cAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTgc                                       >  1:186789/1‑70 (MQ=12)
                            cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                                        >  1:3760587/1‑69 (MQ=255)
                             aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                          >  1:4201841/1‑50 (MQ=255)
                             aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                          >  1:3184393/1‑50 (MQ=255)
                             aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                                     >  1:5664523/1‑71 (MQ=255)
                             aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                                     >  1:254290/1‑71 (MQ=255)
                             aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGAAAGTACCATCGCGATACCGACCAGAgcgc                                     >  1:3427005/1‑71 (MQ=255)
                              gTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGcc                                    >  1:5383800/1‑71 (MQ=12)
                              gTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGcc                                    >  1:786918/1‑71 (MQ=255)
                               tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                                        <  1:1082062/50‑1 (MQ=9)
                               tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                                        <  1:5592764/50‑1 (MQ=9)
                               tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                                        <  1:3242049/50‑1 (MQ=9)
                               tAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa                                                  >  1:1141017/1‑56 (MQ=255)
                               tAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGccc                                   >  1:2052512/1‑71 (MQ=255)
                                aGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCt                                  >  1:1240559/1‑71 (MQ=255)
                                aGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                                  >  1:780975/1‑71 (MQ=255)
                                 gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                                    >  1:5134930/1‑52 (MQ=9)
                                 gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                                    >  1:1058364/1‑52 (MQ=9)
                                 gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                                    >  1:817718/1‑52 (MQ=9)
                                 gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                            <  1:2898020/44‑1 (MQ=255)
                                 gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                                  >  1:1090433/1‑70 (MQ=255)
                                  aaCCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTg                                 >  1:5073295/1‑70 (MQ=9)
                                   aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                                <  1:260009/70‑1 (MQ=255)
                                   aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                                <  1:718203/70‑1 (MQ=255)
                                      gCCAAAGAAGGCCATCGGTACGAATACCGCGGACAGTACCATCGCGATACCGACCaga                                         >  1:3391834/1‑58 (MQ=255)
                                      gCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                            <  1:2642158/71‑1 (MQ=255)
                                        cgaagaatGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGc                          <  1:593814/69‑1 (MQ=255)
                                         aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                                     >  1:5360285/1‑43 (MQ=255)
                                         aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcc                         >  1:1816424/1‑71 (MQ=255)
                                          aagaagGCCATCGGTACGAATACCGCCGACAGTACCa                                                          <  1:3429659/37‑1 (MQ=255)
                                          aagaagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATAcc                                                <  1:2467516/47‑1 (MQ=255)
                                           agaagGCCATCGGTACGAATACCGCCGACAGTACCATcgc                                                      <  1:1871110/40‑1 (MQ=255)
                                             aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGAcc                                            >  1:4923411/1‑48 (MQ=255)
                                             aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                           >  1:4654972/1‑49 (MQ=255)
                                             aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTg                           <  1:3090746/65‑1 (MQ=255)
                                              agGCCATCGGTACGAATACCGCCGACAGTACCATcgc                                                      <  1:4894642/37‑1 (MQ=255)
                                              agGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATAcc                                                <  1:1399055/43‑1 (MQ=255)
                                               tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg                   <  1:2156899/70‑1 (MQ=255)
                                               tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg                   <  1:457399/70‑1 (MQ=255)
                                               ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCg                   <  1:5272128/71‑1 (MQ=255)
                                                gCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                                <  1:905006/57‑1 (MQ=255)
                                                  cATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCTTCGACt                >  1:1866184/1‑71 (MQ=255)
                                                   aTCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt                >  1:1423079/1‑70 (MQ=255)
                                                    tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa              >  1:3063381/1‑71 (MQ=255)
                                                     cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATc                             >  1:4732004/1‑55 (MQ=255)
                                                     cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATc                             >  1:5411668/1‑55 (MQ=255)
                                                      ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg            >  1:4652197/1‑71 (MQ=255)
                                                      ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCAACTTACg            >  1:5107319/1‑71 (MQ=255)
                                                        tACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACgg           <  1:3657130/70‑1 (MQ=255)
                                                         aCGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc             <  1:775211/67‑1 (MQ=255)
                                                          cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg          >  1:370842/1‑69 (MQ=255)
                                                            aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGATTTTGcga                        >  1:3464653/1‑51 (MQ=19)
                                                            aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                  >  1:5636199/1‑59 (MQ=255)
                                                            aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                  >  1:1861955/1‑59 (MQ=255)
                                                            aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                  >  1:3019711/1‑59 (MQ=255)
                                                            aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                  >  1:3216126/1‑59 (MQ=255)
                                                            aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                  >  1:4848865/1‑59 (MQ=255)
                                                             aTACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt                <  1:3574320/60‑1 (MQ=255)
                                                             aTACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt                <  1:4281949/60‑1 (MQ=255)
                                                              tACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                            <  1:2928484/47‑1 (MQ=255)
                                                              tACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                            <  1:4381134/47‑1 (MQ=255)
                                                               aCCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGAttt               <  1:3507797/59‑1 (MQ=255)
                                                               aCCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGAttt               <  1:1629952/59‑1 (MQ=255)
                                                               aCCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc   >  1:433074/1‑71 (MQ=255)
                                                               aCCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc   >  1:1685943/1‑71 (MQ=255)
                                                                ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGc                          >  1:2158641/1‑47 (MQ=255)
                                                                ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttct  >  1:1320568/1‑71 (MQ=255)
                                                                    |                                                                  
GTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCT  >  minE/311455‑311589

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A